Encephalitis/encephalopathy is a rare, but severe, complication of pertussis. Here, we report a case of an unimmunized 7-year-old boy with confirmed pertussis complicated by acute encephalitis/encephalopathy. Eighteen days after the onset of pertussis, generalized seizures began. Magnetic resonance imaging (MRI) indicated that marked demyelination without cytotoxic edema may have occurred to the patient. Notably, this is the first report to show precise MRI findings of pertussis-associated encephalitis/encephalopathy. Markedly increased myelin basic protein levels in the cerebrospinal fluid were consistent with the MRI findings. There was no evidence of direct invasion of the causative bacterium or its products into the central nervous system. The levels of interleukin-6 and -10 in the cerebrospinal fluid were higher than those in serum. Taken together, we conclude that indirect immune-mediated mechanisms may have contributed to the pathogenesis of the encephalitis/encephalopathy.